Where did these ideas come from? Some are seeds which spawned concepts, others are examples of where these same ideas have cropped up independently.
Life: Most things, including deep nesting. I attribute most of the independent consensus to this aspect.
Revelation: The book in the Bible. Axies of merit and paralell spiritual hierarchies.
Dungeon Siege: Linked limitless spatial nodes.
Megatokyo: PCs with emotional stats and independent behavior.
A Fire Upon the Deep: Vast scope fiction and data-intense societal development.
D&D and GURPS: role playing games (a mixture of positive and negative examples in both).
StarTrek Enterprise Floorplans: Vessels really can be fleshed out internally.
Dwarf Fortress: Lots of deep and broad world simulation. Taking over historical characters, etc.